Indonesian security forces have retrieved the bodies of 16 people in the aftermath of a massacre by suspected separatist rebels in restive Papua province, the military said Thursday.

The confirmed deaths, believed to be of construction workers, mark the deadliest bout of violence in years to hit a region wracked by a low-level independence insurgency.

The bodies will be evacuated to the town of Timika from the remote district of Nduga, a mountainous region where the attack happened Sunday, local military commander Binsar Panjaitan said.

"The latest information is that 16 bodies have been found," Panjaitan told reporters in Papua.

The dead had not been identified and the military did not supply details about how they were killed.

An earlier eyewitness account supplied by the military detailed the killing of at least 19 people, including in execution style shootings or having their throat slit.

Previous local media reports put the number of dead between 24 and 31.

On Thursday, the military warned that it was not yet clear whether all the dead worked for a state-owned contractor that has been building bridges and roads as part of efforts to boost infrastructure in the impoverished region.

Another 15 people -- including seven employees of the contractor -- have been evacuated from the area.

Many in Papua view Indonesia as a colonial occupier and its building work as a way to exert more control over a region that shares a border with Papua New Guinea, an independent nation.

Police and military teams sent to the area have come under rebel gunfire with one soldier killed and two wounded since Monday, according to authorities.

On Wednesday, the military supplied an account from one survivor identified by his initials "JA" who claimed about 50 rebels entered the workers' camp on Saturday and led them away with their hands tied behind their backs.

The following day, the rebels shot dead a group of workers, while some tried to escape, the account said.

The attackers allegedly recaptured six workers and slit their throats, according to the uninjured witness, who said at least 19 employees had been killed in all.

A Facebook account purportedly run by the National Liberation Army of West Papua (TPNPB) said the armed group had killed 24 workers on the orders of regional commander Ekianus Kogoya.

Indonesia routinely blames separatists for violence in Papua and foreign media need permission to report there, making it difficult to obtain reliable information.

Papua declared itself an independent nation from the Dutch in 1961, but neighbouring Indonesia took control of the resource-rich region two years later on the condition it hold an independence referendum.

It officially annexed Papua in 1969 with a UN-backed vote, widely seen as a sham.